Replica sub-permutation method for molecular dynamics and monte carlo simulations

Journal of Computational Chemistry
Masataka Yamauchi, Hisashi Okumura

Abstract

We propose an improvement of the replica-exchange and replica-permutation methods, which we call the replica sub-permutation method (RSPM). Instead of considering all permutations, this method uses a new algorithm referred to as sub-permutation to perform parameter transition. The RSPM succeeds in reducing the number of combinations between replicas and parameters without the loss of sampling efficiency. For comparison, we applied the replica sub-permutation, replica-permutation, and replica-exchange methods to a β-hairpin mini protein, chignolin, in explicit water. We calculated the transition ratio and number of tunneling events in the parameter space, the number of folding-unfolding events, the autocorrelation function, and the autocorrelation time as measures of sampling efficiency. The results indicate that among the three methods, the proposed RSPM is the most efficient in both parameter and conformational spaces. © 2019 Wiley Periodicals, Inc.

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Citations

May 23, 2019·Biophysics Reviews·Masataka YamauchiHisashi Okumura
Aug 2, 2020·Proceedings of the National Academy of Sciences of the United States of America·Takuya MizukamiKosuke Maki
Jan 23, 2021·The Journal of Chemical Physics·Hisashi Okumura, Satoru G Itoh
Feb 25, 2021·Journal of Chemical Information and Modeling·Masataka Yamauchi, Hisashi Okumura
Mar 7, 2021·International Journal of Molecular Sciences·Satoru G Itoh, Hisashi Okumura

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